Comparative analysis of racial differences in breast tumor microbiome/Experiment 3

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Reviewed Marked as Reviewed by Chloe on 2022/03/15

Curated date: 2021/07/22

Curator: Itslanapark

Revision editor(s): Itslanapark, WikiWorks, Victoria

Subjects

Location of subjects

United States of America

Host species Species from which microbiome was sampled. Contact us to have more species added.

Homo sapiens

Body site Anatomical site where microbial samples were extracted from according to the Uber Anatomy Ontology

Breast Mamma,Mammary part of chest,Mammary region,Breast,breast

Condition The experimental condition / phenotype studied according to the Experimental Factor Ontology

Neoplasm cell process disease,disease of cellular proliferation,neoplasia,neoplasm,neoplasm (disease),neoplastic disease,neoplastic growth,other neoplasm,tumor,tumor disease,Neoplasm

Group 0 name Corresponds to the control (unexposed) group for case-control studies

WNH with TNBC normal tissue (second set)

Group 1 name Corresponds to the case (exposed) group for case-control studies

WNH with TNBC normal tissue (second set)

Group 1 definition Diagnostic criteria applied to define the specific condition / phenotype represented in the case (exposed) group

Tumor tissue from white non-hispanic patients with triple negative breast cancer

Group 0 sample size Number of subjects in the control (unexposed) group

10

Group 1 sample size Number of subjects in the case (exposed) group

10

Antibiotics exclusion Number of days without antibiotics usage (if applicable) and other antibiotics-related criteria used to exclude participants (if any)

Biorepository information revealed that no patients were treated with antibiotics prior to tissue sample collection, however duration window of non-exposure was unidentified.

Lab analysis

Sequencing type

16S

16S variable region One or more hypervariable region(s) of the bacterial 16S gene

V3-V4

Sequencing platform Manufacturer and experimental platform used for quantifying microbial abundance

Illumina

Statistical Analysis

Data transformation Data transformation applied to microbial abundance measurements prior to differential abundance testing (if any).

relative abundances

Statistical test

Mann-Whitney (Wilcoxon)

Significance threshold p-value or FDR threshold used for differential abundance testing (if any)

0.05

MHT correction Have statistical tests be corrected for multiple hypothesis testing (MHT)?

No

Alpha Diversity

Shannon Estimator of species richness and species evenness: more weight on species richness

increased

Chao1 Abundance-based estimator of species richness

increased

Richness Number of species

increased